Y `earlier’ mutations happened in vivo, and all driver mutations will

Y `earlier’ mutations happened in vivo, and all driver mutations will be in the `earlier’ set, whereas if endoreduplication happened in vivo (as is often the case in breast tumours [17]), some driving mutations will be present in the `later’ group. In either case our estimate of nonrandomly timed mutations remains the same.Comparison with Mutations in Breast CancersTo attempt to identify mutations in HCC1187 that are recurrent or known drivers, and relate this to timing, we compared sequencing data from breast tumours, both genomic sequencing data [29,31,39?1] and fusion gene data from transcriptome sequencing [15,42]. However, this was largely uninformative, because of the heterogeneity and variability of mutations among cancer cases, and the still limited amount of data available. For example, Stephens et al [29] identified 31 genes as targets of driver mutations in breast cancers, from sequencing of 100 exomes and comparison with known On was added to 100 ml of TE buffer (10 mM Tris-HCl, 1 mM drivers in other cancers, but the individual tumours had an average of only 1.7 of these genes mutated, 1.3 if TP53 is excluded. Unsurprisingly, then, in HCC1187 only two of these drivers, TP53 and BAP1, were mutated (both earlier). Similarly, of the genes considered likely drivers by Shah et al [31] in triple negative breast cancers, only SYNE2 and TP53 were mutated in HCC1187 YNE2 is fused, also earlier. Nevertheless, many other genes mutated in HCC1187 are mutated or rearranged occasionally in the datasets above, so may be recurrent at a modest level (Tables S4, S7 in File S2). Several genes involved in fusions 18204824 have been reported to be fused or rearranged in other cases GPAT5, NOTCH2, PUM1, SEC22B, SGK1 and TRERF1 (all early or unclassified), while several are mutated at sequence level, notably SYNE2. Among the genes in homozygous deletions (all earlier) with four or more reported mutations or rearrangements were SCN1A, FBXL20 and MYO9A; while among the point-mutated genes in HCC1187, apart fromTiming and Evidence for SelectionA non-random distribution of mutations between Title Loaded From File earlier and later categories could be evidence that a substantial number of mutations were drivers rather than passengers. The group of mutations showing greatest deviation from the typical pattern of around 40 earlier was the truncating mutations (and especially indels). A non-random distribution could be explained in two ways: i) the rate of indel mutations was high before endoreduplication and low after, relative to most other types of mutation ii) passenger indels accumulated in the same way as other passenger mutations but more indels accumulated early because they were selected. We consider (ii) most likely because for 9/11 earlier truncating mutations, a chromosome loss before endoreduplication caused loss of the second wild type allele. This is consistent with chromosome instability facilitating early tumor suppressor loss, as has been suggested previously [21]. Indeed, the earlier truncation mutations include known and candidate tumor suppressor genes TP53, BAP1 (BRCA1-associated protein), CTNNA1 (CateninA1) and NFKBIA (nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor) [20,29,32?4];Timing of Mutations in a Breast Cancer Genomethe known drivers BAP1 and TP53, ones with four or more reported mutations or rearrangements were CAMTA1, ITIH6/ ITIH5L, LHCGR, SPEN, TP53 and ZNF142 (3 of which were earlier, 3 later). Many of the other genes have been found mutated in cancers other than breast, includin.Y `earlier’ mutations happened in vivo, and all driver mutations will be in the `earlier’ set, whereas if endoreduplication happened in vivo (as is often the case in breast tumours [17]), some driving mutations will be present in the `later’ group. In either case our estimate of nonrandomly timed mutations remains the same.Comparison with Mutations in Breast CancersTo attempt to identify mutations in HCC1187 that are recurrent or known drivers, and relate this to timing, we compared sequencing data from breast tumours, both genomic sequencing data [29,31,39?1] and fusion gene data from transcriptome sequencing [15,42]. However, this was largely uninformative, because of the heterogeneity and variability of mutations among cancer cases, and the still limited amount of data available. For example, Stephens et al [29] identified 31 genes as targets of driver mutations in breast cancers, from sequencing of 100 exomes and comparison with known drivers in other cancers, but the individual tumours had an average of only 1.7 of these genes mutated, 1.3 if TP53 is excluded. Unsurprisingly, then, in HCC1187 only two of these drivers, TP53 and BAP1, were mutated (both earlier). Similarly, of the genes considered likely drivers by Shah et al [31] in triple negative breast cancers, only SYNE2 and TP53 were mutated in HCC1187 YNE2 is fused, also earlier. Nevertheless, many other genes mutated in HCC1187 are mutated or rearranged occasionally in the datasets above, so may be recurrent at a modest level (Tables S4, S7 in File S2). Several genes involved in fusions 18204824 have been reported to be fused or rearranged in other cases GPAT5, NOTCH2, PUM1, SEC22B, SGK1 and TRERF1 (all early or unclassified), while several are mutated at sequence level, notably SYNE2. Among the genes in homozygous deletions (all earlier) with four or more reported mutations or rearrangements were SCN1A, FBXL20 and MYO9A; while among the point-mutated genes in HCC1187, apart fromTiming and Evidence for SelectionA non-random distribution of mutations between earlier and later categories could be evidence that a substantial number of mutations were drivers rather than passengers. The group of mutations showing greatest deviation from the typical pattern of around 40 earlier was the truncating mutations (and especially indels). A non-random distribution could be explained in two ways: i) the rate of indel mutations was high before endoreduplication and low after, relative to most other types of mutation ii) passenger indels accumulated in the same way as other passenger mutations but more indels accumulated early because they were selected. We consider (ii) most likely because for 9/11 earlier truncating mutations, a chromosome loss before endoreduplication caused loss of the second wild type allele. This is consistent with chromosome instability facilitating early tumor suppressor loss, as has been suggested previously [21]. Indeed, the earlier truncation mutations include known and candidate tumor suppressor genes TP53, BAP1 (BRCA1-associated protein), CTNNA1 (CateninA1) and NFKBIA (nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor) [20,29,32?4];Timing of Mutations in a Breast Cancer Genomethe known drivers BAP1 and TP53, ones with four or more reported mutations or rearrangements were CAMTA1, ITIH6/ ITIH5L, LHCGR, SPEN, TP53 and ZNF142 (3 of which were earlier, 3 later). Many of the other genes have been found mutated in cancers other than breast, includin.